Contacts of the helix formed by residues 63 - 76 (chain C) in PDB entry 1P7L
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 63 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A TRP* 4.5 8.2 - - + -
97A LYS* 2.6 33.2 + - - -
62C VAL* 1.3 74.1 - - - +
64C ILE* 1.3 58.0 + - - +
65C GLU* 3.2 18.9 + - - +
66C GLU* 3.4 22.7 + - + +
67C ILE* 3.0 36.4 + - + +
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Residues in contact with ILE 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C VAL* 4.3 22.0 - - + -
52C VAL* 3.6 32.1 - - + -
56C ILE* 5.8 1.6 - - + -
62C VAL* 3.9 26.0 + - + +
63C ASP* 1.3 69.8 + - - +
65C GLU* 1.3 58.9 + - - +
67C ILE* 4.0 4.3 - - + +
68C THR* 2.5 40.2 + - - +
91C VAL* 4.5 4.3 - - + -
93C SER* 3.6 23.3 - - - +
95C ILE* 4.1 22.9 - - + -
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Residues in contact with GLU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ILE 4.1 8.6 - - - +
96A GLY* 3.3 29.7 - - - -
97A LYS* 3.9 14.2 + - - +
47B THR* 5.8 0.5 - - - +
63C ASP* 3.2 9.3 + - - +
64C ILE* 1.3 77.9 - - - +
66C GLU* 1.3 69.4 + - - +
68C THR* 3.5 0.2 - - - -
69C ARG* 2.5 81.3 + - - +
91C VAL* 3.9 21.7 - - + +
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Residues in contact with GLU 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LYS* 2.8 33.6 + - - +
63C ASP* 3.4 23.0 + - + +
65C GLU* 1.3 88.1 - - - +
67C ILE* 1.3 67.1 - - + +
69C ARG* 4.6 8.1 - - - +
70C ASN* 2.9 46.0 + - - +
73C ARG* 5.6 1.4 + - - -
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Residues in contact with ILE 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE* 4.9 1.3 - - + +
25C ALA* 3.8 35.9 - - + +
26C VAL* 4.0 17.7 - - + -
29C ALA* 3.5 30.3 - - + -
62C VAL* 4.0 15.3 - - + -
63C ASP* 3.0 31.2 + - + +
64C ILE* 4.0 4.5 - - - +
66C GLU* 1.3 76.4 - - + +
68C THR* 1.3 57.0 + - - +
70C ASN* 3.9 4.4 - - - +
71C THR* 2.7 37.1 + - - +
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Residues in contact with THR 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE* 3.5 20.3 - - + +
26C VAL* 5.2 0.3 - - - +
50C VAL* 3.5 37.0 - - + -
52C VAL* 3.9 7.1 - - - +
64C ILE* 2.5 36.1 + - - +
65C GLU 3.5 2.7 - - - -
67C ILE* 1.3 76.2 - - - +
69C ARG* 1.3 67.9 + - - +
71C THR* 2.8 17.7 + - - -
72C VAL* 2.9 14.9 + - + +
89C CYS* 5.8 1.6 - - - -
91C VAL* 4.1 16.3 - - + +
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Residues in contact with ARG 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B THR* 3.8 22.6 + - - +
65C GLU* 2.5 57.6 + - + +
66C GLU* 4.1 9.4 - - - +
68C THR* 1.3 72.5 - - - +
70C ASN* 1.3 52.0 + - - +
72C VAL* 4.8 1.6 - - - -
73C ARG* 2.7 52.3 + - - +
86C ALA* 2.6 47.6 + - - +
87C ASN* 3.5 15.8 + - - +
89C CYS* 2.5 45.0 + - - +
91C VAL* 3.7 18.2 - - + +
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Residues in contact with ASN 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C GLU* 2.9 40.9 + - - +
67C ILE* 3.9 4.6 - - - +
69C ARG* 1.3 77.0 - - - +
71C THR* 1.3 64.7 + - - +
73C ARG* 2.6 36.0 + - - +
74C GLU* 3.0 39.4 + - - +
352C LYS* 6.2 0.2 - - - +
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Residues in contact with THR 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLN* 4.1 15.9 - - + -
22C ILE* 4.0 32.5 - - + +
25C ALA* 3.3 13.3 - - - +
67C ILE* 2.7 23.6 + - - +
68C THR* 2.8 8.9 + - - -
70C ASN* 1.3 78.5 - - - +
72C VAL* 1.3 61.5 + - - +
74C GLU* 3.4 4.3 + - - +
75C ILE* 3.1 23.8 + - + +
352C LYS* 3.2 29.3 + - + +
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Residues in contact with VAL 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ILE* 4.0 28.7 - - + -
22C ILE* 4.1 15.0 - - + -
50C VAL* 4.8 3.1 - - + -
68C THR* 2.9 13.6 + - + +
69C ARG* 3.9 2.2 - - - +
71C THR* 1.3 73.7 - - - +
73C ARG* 1.3 71.6 + - - +
75C ILE* 2.7 23.7 + - + +
76C GLY 3.0 8.3 + - - -
77C TYR* 3.8 14.2 + - + +
84C PHE* 4.3 25.4 - - + -
86C ALA* 3.3 30.3 - - + +
89C CYS* 5.7 1.6 - - - -
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Residues in contact with ARG 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C GLU* 5.6 1.4 + - - -
69C ARG* 2.7 37.6 + - - +
70C ASN* 2.6 44.1 + - - +
72C VAL* 1.3 72.3 - - - +
74C GLU* 1.3 66.7 + - - +
76C GLY* 2.9 18.2 + - - -
78C VAL* 3.9 22.8 - - + +
86C ALA* 3.6 9.4 - - + -
87C ASN* 3.2 40.2 + - - +
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Residues in contact with GLU 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C GLU* 4.9 0.7 - - - -
70C ASN* 3.0 33.0 + - - +
71C THR* 3.7 4.9 - - - +
72C VAL 3.2 0.2 - - - -
73C ARG* 1.3 75.7 - - - +
75C ILE* 1.3 69.6 + - - +
76C GLY* 3.2 1.6 + - - -
153C LYS* 3.9 16.3 + - - -
352C LYS* 3.8 22.6 + - - +
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Residues in contact with ILE 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C GLU* 3.6 37.4 - - + +
13C GLY* 3.9 14.8 - - - -
18C ILE* 4.1 27.8 - - + -
21C GLN* 3.8 24.0 - - + +
71C THR* 3.1 29.7 + - + +
72C VAL* 2.7 24.2 + - - +
74C GLU* 1.3 73.4 - - - +
76C GLY* 1.3 58.0 + - - +
77C TYR* 4.1 19.1 - - + -
152C ARG* 2.8 26.2 + - - -
162C PRO* 4.3 1.5 - - + +
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Residues in contact with GLY 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C VAL 3.0 1.4 + - - -
73C ARG 2.9 14.6 + - - -
74C GLU 4.0 1.1 - - - -
75C ILE* 1.3 80.4 - - - +
77C TYR* 1.3 60.2 + - - +
78C VAL* 3.0 21.7 + - - +
82C MET* 3.5 10.0 - - - +
152C ARG* 4.6 3.4 - - - -
162C PRO* 3.8 13.5 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il